YBFQ - BACSU - GREMLIN Contacts

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YBFQ - UPF0176 protein YbfQ

UniProt:	O31457	Sequences: MEKQYRVLLYYKYVPIEDPEAFREQHLAFCKELGLLGRILVSSEGINGTVSGTVEQTEKYMETMKADPRFADMVFKIDEAEGHAFKKIFVRHKKELVTLRLEDDVDPNETTGQHLKPAEFYEKMQDPNTIVIDARNDYEYDLGHFRGAVRPDIEAFRELPEWIEEHKDMLEGKKILTYCTGGVRCEKFSGWLVKQGFEDVAQLDGGIVTYGKDPEVQGKLWDGQCYVFDERISVPVNRVEHVIVGKDYFTGEPCERYVNCANPSCNKKMICTPENEYKYMRSCSHECRTNPRNLYVKEHNMTEEEVNARLAAIETEDHAAAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	322 (291)
Sequences:	1626 (912)
Seq/√Len:	53.5

ECOLI - YCEA
BACSU - YBFQ

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
146_R	222_D	5.430	1.00
116_K	204_D	5.064	1.00
164_E	195_Q	4.450	1.00
50_V	60_Y	4.424	1.00
142_L	233_S	3.871	1.00
144_H	178_Y	3.163	1.00
118_A	213_D	3.062	1.00
30_C	88_I	2.853	1.00
125_Q	220_L	2.842	1.00
18_D	21_A	2.733	1.00
19_P	92_H	2.725	1.00
161_E	165_E	2.724	1.00
12_K	72_D	2.699	1.00
114_H	202_Q	2.621	1.00
235_P	240_E	2.559	1.00
34_G	56_Q	2.501	1.00
267_K	288_R	2.497	1.00
6_R	54_V	2.380	1.00
27_L	31_K	2.360	1.00
10_Y	39_I	2.347	1.00
272_T	275_N	2.334	1.00
74_V	204_D	2.280	1.00
10_Y	48_G	2.256	1.00
191_W	195_Q	2.254	1.00
54_V	77_I	2.215	1.00
261_A	273_P	2.202	1.00
54_V	58_E	2.184	1.00
164_E	191_W	2.124	1.00
208_V	225_C	2.083	1.00
35_L	60_Y	2.069	1.00
58_E	62_E	2.064	1.00
116_K	119_E	2.018	1.00
209_T	213_D	2.007	1.00
51_S	84_A	1.997	1.00
29_F	33_L	1.986	1.00
254_C	259_N	1.981	1.00
279_Y	284_S	1.967	1.00
250_T	275_N	1.917	1.00
283_C	287_C	1.911	1.00
28_A	32_E	1.908	0.99
174_K	199_D	1.884	0.99
6_R	58_E	1.862	0.99
146_R	220_L	1.858	0.99
115_L	119_E	1.842	0.99
65_K	72_D	1.825	0.99
250_T	272_T	1.820	0.99
120_F	203_L	1.812	0.99
230_E	248_Y	1.761	0.99
141_D	274_E	1.759	0.99
53_T	56_Q	1.723	0.99
167_K	171_E	1.703	0.99
291_P	295_Y	1.698	0.99
137_D	154_E	1.697	0.99
24_E	28_A	1.688	0.99
106_D	109_E	1.680	0.99
224_Q	243_I	1.678	0.99
289_T	292_R	1.659	0.99
245_G	259_N	1.657	0.99
263_P	276_E	1.624	0.98
35_L	50_V	1.622	0.98
257_Y	270_I	1.587	0.98
61_M	75_F	1.587	0.98
110_T	193_V	1.557	0.98
141_D	150_R	1.516	0.97
126_D	129_T	1.442	0.96
130_I	175_I	1.434	0.96
295_Y	299_H	1.432	0.96
61_M	77_I	1.429	0.96
247_D	250_T	1.410	0.96
252_E	278_K	1.406	0.96
26_H	60_Y	1.405	0.96
35_L	88_I	1.385	0.96
27_L	88_I	1.376	0.95
120_F	176_L	1.374	0.95
167_K	192_L	1.370	0.95
209_T	212_K	1.360	0.95
285_H	288_R	1.357	0.95
33_L	56_Q	1.355	0.95
23_R	92_H	1.352	0.95
247_D	275_N	1.346	0.95
8_L	57_T	1.345	0.95
216_V	237_N	1.339	0.95
175_I	197_F	1.328	0.94
291_P	294_L	1.328	0.94
124_M	176_L	1.319	0.94
19_P	43_S	1.319	0.94
134_A	159_L	1.318	0.94
294_L	298_E	1.307	0.94
86_K	230_E	1.294	0.94
29_F	63_T	1.291	0.93
74_V	209_T	1.290	0.93
169_M	172_G	1.285	0.93
247_D	272_T	1.283	0.93
129_T	174_K	1.282	0.93
121_Y	219_K	1.277	0.93
285_H	289_T	1.270	0.93
119_E	122_E	1.266	0.93
153_I	159_L	1.238	0.92
33_L	59_K	1.226	0.92
280_M	283_C	1.216	0.91
122_E	126_D	1.205	0.91
113_Q	193_V	1.201	0.91
224_Q	242_V	1.199	0.91
140_Y	150_R	1.196	0.91
65_K	73_M	1.187	0.90
258_V	273_P	1.163	0.89
35_L	57_T	1.162	0.89
166_H	169_M	1.156	0.89
190_G	193_V	1.151	0.89
44_E	187_K	1.150	0.89
6_R	79_E	1.148	0.89
101_L	104_D	1.145	0.89
167_K	170_L	1.141	0.88
189_S	202_Q	1.141	0.88
111_T	202_Q	1.102	0.87
252_E	274_E	1.102	0.87
249_F	271_C	1.097	0.86
65_K	71_A	1.082	0.86
155_A	158_E	1.081	0.86
123_K	201_A	1.081	0.86
115_L	123_K	1.078	0.85
193_V	198_E	1.070	0.85
51_S	83_H	1.052	0.84
6_R	77_I	1.052	0.84
226_Y	268_K	1.051	0.84
7_V	80_A	1.047	0.84
172_G	198_E	1.046	0.84
20_E	43_S	1.041	0.83
243_I	255_E	1.039	0.83
188_F	192_L	1.037	0.83
99_L	156_F	1.037	0.83
97_V	157_R	1.035	0.83
16_I	70_F	1.012	0.81
235_P	241_H	1.003	0.81
239_V	242_V	0.997	0.81
16_I	22_F	0.997	0.81
124_M	131_V	0.990	0.80
258_V	281_R	0.989	0.80
31_K	88_I	0.988	0.80
132_I	163_I	0.982	0.79
18_D	69_R	0.981	0.79
279_Y	287_C	0.972	0.79
29_F	32_E	0.957	0.78
31_K	34_G	0.957	0.78
121_Y	220_L	0.947	0.77
163_I	197_F	0.941	0.77
114_H	204_D	0.940	0.76
63_T	66_A	0.938	0.76
65_K	75_F	0.934	0.76
122_E	125_Q	0.924	0.75
100_R	157_R	0.923	0.75
15_P	43_S	0.915	0.74
263_P	273_P	0.914	0.74
29_F	56_Q	0.909	0.74
24_E	31_K	0.909	0.74
245_G	270_I	0.906	0.74
23_R	41_V	0.906	0.74
281_R	298_E	0.903	0.73
271_C	276_E	0.899	0.73
9_L	49_T	0.899	0.73
21_A	25_Q	0.898	0.73
245_G	254_C	0.896	0.73
61_M	73_M	0.891	0.72
67_D	70_F	0.890	0.72
41_V	92_H	0.882	0.72
30_C	60_Y	0.879	0.71
219_K	239_V	0.878	0.71
294_L	297_K	0.877	0.71
29_F	35_L	0.875	0.71
120_F	131_V	0.872	0.71
16_I	19_P	0.870	0.71
7_V	49_T	0.870	0.71
168_D	171_E	0.868	0.70
112_G	200_V	0.863	0.70
214_P	219_K	0.860	0.70
102_E	110_T	0.855	0.69
8_L	75_F	0.854	0.69
30_C	39_I	0.851	0.69
78_D	212_K	0.849	0.69
130_I	172_G	0.847	0.69
208_V	212_K	0.841	0.68
136_N	184_R	0.841	0.68
279_Y	288_R	0.837	0.68
86_K	251_G	0.835	0.68
284_S	287_C	0.832	0.67
120_F	202_Q	0.824	0.66
244_V	255_E	0.824	0.66
224_Q	255_E	0.819	0.66
235_P	255_E	0.816	0.66
14_V	69_R	0.815	0.66
241_H	255_E	0.813	0.65
167_K	172_G	0.811	0.65
96_L	100_R	0.809	0.65
167_K	197_F	0.809	0.65
14_V	70_F	0.808	0.65
177_T	226_Y	0.802	0.64
292_R	296_V	0.801	0.64
61_M	65_K	0.800	0.64
123_K	174_K	0.791	0.63
40_L	49_T	0.788	0.63
99_L	105_V	0.780	0.62
44_E	96_L	0.780	0.62
260_C	287_C	0.779	0.62
204_D	233_S	0.778	0.62
151_P	162_W	0.776	0.62
256_R	259_N	0.773	0.61
126_D	174_K	0.770	0.61
156_F	227_V	0.770	0.61
264_S	290_N	0.765	0.61
218_G	240_E	0.762	0.60
49_T	95_E	0.762	0.60
121_Y	214_P	0.761	0.60
233_S	242_V	0.761	0.60
121_Y	125_Q	0.759	0.60
19_P	25_Q	0.757	0.60
101_L	105_V	0.755	0.60
107_P	111_T	0.755	0.60
142_L	232_I	0.751	0.59
70_F	197_F	0.751	0.59
16_I	41_V	0.749	0.59
162_W	167_K	0.748	0.59
34_G	83_H	0.746	0.59
54_V	79_E	0.745	0.59
28_A	31_K	0.744	0.59
50_V	88_I	0.743	0.58
217_Q	239_V	0.740	0.58
168_D	172_G	0.736	0.58
119_E	278_K	0.733	0.57
29_F	59_K	0.732	0.57
74_V	116_K	0.732	0.57
96_L	227_V	0.729	0.57
49_T	97_V	0.729	0.57
268_K	295_Y	0.727	0.57
186_E	202_Q	0.724	0.56
13_Y	120_F	0.724	0.56
28_A	63_T	0.718	0.56
76_K	209_T	0.718	0.56
110_T	194_K	0.715	0.56
263_P	277_Y	0.713	0.55
6_R	53_T	0.713	0.55
8_L	50_V	0.712	0.55
27_L	34_G	0.711	0.55
16_I	67_D	0.708	0.55
140_Y	144_H	0.705	0.54
112_G	193_V	0.704	0.54
13_Y	225_C	0.703	0.54
123_K	176_L	0.703	0.54
59_K	62_E	0.701	0.54
150_R	154_E	0.698	0.54
24_E	27_L	0.696	0.54
281_R	288_R	0.696	0.54
233_S	294_L	0.696	0.54
163_I	166_H	0.695	0.53
35_L	52_G	0.693	0.53
177_T	189_S	0.691	0.53
282_S	287_C	0.689	0.53
169_M	197_F	0.686	0.52
43_S	92_H	0.684	0.52
50_V	56_Q	0.684	0.52
19_P	41_V	0.684	0.52
151_P	221_W	0.682	0.52
248_Y	268_K	0.682	0.52
113_Q	119_E	0.680	0.52
132_I	151_P	0.680	0.52
127_P	132_I	0.678	0.52
85_F	183_V	0.678	0.52
217_Q	237_N	0.677	0.52
86_K	91_R	0.676	0.51
154_E	158_E	0.676	0.51
237_N	240_E	0.673	0.51
21_A	31_K	0.673	0.51
279_Y	283_C	0.671	0.51
22_F	41_V	0.670	0.51
93_K	157_R	0.668	0.51
23_R	31_K	0.668	0.51
251_G	297_K	0.664	0.50
165_E	170_L	0.664	0.50
134_A	188_F	0.663	0.50
249_F	269_M	0.661	0.50
56_Q	59_K	0.660	0.50
246_K	268_K	0.660	0.50
8_L	147_G	0.656	0.49
112_G	190_G	0.654	0.49
32_E	258_V	0.651	0.49
9_L	76_K	0.650	0.49
7_V	84_A	0.650	0.49
259_N	262_N	0.647	0.48
152_D	158_E	0.647	0.48
252_E	273_P	0.647	0.48
96_L	163_I	0.646	0.48
119_E	152_D	0.644	0.48
295_Y	298_E	0.644	0.48
142_L	246_K	0.643	0.48
134_A	192_L	0.643	0.48
208_V	224_Q	0.643	0.48
131_V	220_L	0.641	0.48
13_Y	243_I	0.640	0.48
132_I	167_K	0.640	0.48
192_L	195_Q	0.639	0.47
12_K	75_F	0.635	0.47
5_Y	80_A	0.635	0.47
31_K	56_Q	0.633	0.47
166_H	172_G	0.632	0.47
137_D	150_R	0.631	0.47
94_K	198_E	0.629	0.46
163_I	167_K	0.628	0.46
56_Q	60_Y	0.626	0.46
112_G	189_S	0.626	0.46
98_T	233_S	0.622	0.46
211_G	236_V	0.621	0.46
5_Y	53_T	0.620	0.45
245_G	256_R	0.618	0.45
128_N	173_K	0.617	0.45
293_N	296_V	0.613	0.45
267_K	271_C	0.613	0.45
42_S	94_K	0.613	0.45
273_P	277_Y	0.612	0.45
237_N	241_H	0.611	0.45
30_C	46_I	0.610	0.44
148_A	196_G	0.609	0.44
166_H	170_L	0.608	0.44
68_P	71_A	0.607	0.44
10_Y	251_G	0.606	0.44
225_C	234_V	0.606	0.44
9_L	48_G	0.604	0.44
9_L	13_Y	0.603	0.44
59_K	105_V	0.601	0.44
80_A	86_K	0.599	0.43
39_I	48_G	0.598	0.43
121_Y	176_L	0.598	0.43
30_C	52_G	0.596	0.43
129_T	132_I	0.596	0.43
257_Y	260_C	0.593	0.43
222_D	242_V	0.592	0.43
118_A	217_Q	0.591	0.42
95_E	159_L	0.590	0.42
277_Y	284_S	0.588	0.42
23_R	27_L	0.587	0.42
30_C	35_L	0.585	0.42
147_G	221_W	0.585	0.42
114_H	120_F	0.584	0.42
256_R	273_P	0.583	0.42
104_D	108_N	0.581	0.41
249_F	278_K	0.580	0.41
42_S	96_L	0.578	0.41
131_V	203_L	0.578	0.41
141_D	155_A	0.578	0.41
114_H	189_S	0.577	0.41
48_G	159_L	0.573	0.41
132_I	189_S	0.572	0.41
111_T	190_G	0.571	0.40
130_I	173_K	0.569	0.40
26_H	35_L	0.568	0.40
72_D	216_V	0.567	0.40
34_G	161_E	0.566	0.40
142_L	255_E	0.566	0.40
117_P	209_T	0.563	0.40
14_V	40_L	0.563	0.40
13_Y	159_L	0.562	0.39
138_Y	156_F	0.561	0.39
18_D	67_D	0.561	0.39
17_E	278_K	0.560	0.39
246_K	289_T	0.557	0.39
87_K	157_R	0.554	0.39
121_Y	242_V	0.553	0.39
14_V	117_P	0.553	0.39
27_L	33_L	0.550	0.38
260_C	283_C	0.550	0.38
118_A	193_V	0.550	0.38
256_R	260_C	0.549	0.38
28_A	55_E	0.549	0.38
72_D	147_G	0.549	0.38
216_V	222_D	0.548	0.38
41_V	69_R	0.548	0.38
22_F	63_T	0.546	0.38
105_V	194_K	0.545	0.38
48_G	97_V	0.545	0.38
128_N	174_K	0.545	0.38
226_Y	246_K	0.544	0.38
111_T	114_H	0.543	0.38
269_M	272_T	0.543	0.38
33_L	60_Y	0.541	0.37
29_F	60_Y	0.539	0.37
287_C	294_L	0.539	0.37
167_K	224_Q	0.538	0.37
52_G	57_T	0.536	0.37
232_I	268_K	0.536	0.37
84_A	187_K	0.535	0.37
189_S	193_V	0.535	0.37
128_N	172_G	0.534	0.37
41_V	54_V	0.534	0.37
166_H	173_K	0.531	0.36
144_H	244_V	0.531	0.36
76_K	159_L	0.531	0.36
14_V	67_D	0.531	0.36
159_L	250_T	0.530	0.36
218_G	243_I	0.530	0.36
183_V	257_Y	0.529	0.36
71_A	81_E	0.528	0.36
13_Y	101_L	0.527	0.36
126_D	168_D	0.527	0.36
196_G	200_V	0.527	0.36
81_E	241_H	0.526	0.36
94_K	101_L	0.525	0.36
274_E	286_E	0.524	0.36
278_K	284_S	0.522	0.36
13_Y	208_V	0.520	0.35
76_K	212_K	0.519	0.35
119_E	273_P	0.519	0.35
137_D	193_V	0.516	0.35
109_E	194_K	0.516	0.35
111_T	193_V	0.514	0.35
148_A	155_A	0.512	0.35
107_P	134_A	0.512	0.35
91_R	162_W	0.512	0.35
36_L	40_L	0.511	0.34
163_I	170_L	0.511	0.34
203_L	227_V	0.509	0.34
37_G	45_G	0.508	0.34
88_I	192_L	0.508	0.34
153_I	163_I	0.507	0.34
96_L	187_K	0.506	0.34
76_K	95_E	0.504	0.34
10_Y	35_L	0.503	0.34
40_L	93_K	0.502	0.34
10_Y	60_Y	0.502	0.34
243_I	246_K	0.502	0.34
258_V	274_E	0.502	0.34
99_L	134_A	0.502	0.34
105_V	190_G	0.501	0.34
158_E	280_M	0.501	0.34
78_D	82_G	0.501	0.34
171_E	222_D	0.501	0.34
81_E	94_K	0.500	0.33
28_A	87_K	0.500	0.33
162_W	169_M	0.500	0.33

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4f67A	1	0.7919	100	0.487	Contact Map
1gmxA	1	0.3354	99.7	0.853	Contact Map
2fsxA	1	0.3634	99.6	0.858	Contact Map
1qb0A	1	0.4876	99.6	0.86	Contact Map
1veeA	1	0.3851	99.6	0.861	Contact Map
3g5jA	1	0.3137	99.6	0.861	Contact Map
3icsA	2	0.6398	99.6	0.861	Contact Map
3fojA	1	0.3075	99.6	0.862	Contact Map
3d1pA	1	0.3447	99.6	0.863	Contact Map
1qxnA	2	0.413	99.6	0.863	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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